Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

3,738 thoughts on “Common Design vs. Common Descent

  1. John Harshman: New features are not part of the model of common descent. It’s the nested hierarchy of new features that offers evidence for common descent.

    #EvolutionLogic

  2. At the bottom is an example of an alignment that supposedly is comparable to the hidden Markov Models, it is MUSCLE. I used it to align 4 nylonase genes, 3 of which have evidence of actual nylonase enzymatic activity, not to mention, the genes are have the same name, namely, NylB (for nylonase B).

    The funny capitalization is the result of me pulling the data from UNIRPOT vs. GenBank.

    I used the MUSCLE alignment on the Clustal Server:
    https://www.ebi.ac.uk/Tools/msa/muscle/

    >NylB KI72
    mnarstgqhp arypgaaage ptldswqeap hnrwafarlg ellptaavsr rdpatpaepv
    vrldalatrl pdleqrleet ctdaflvlrg sevlaeyyra gfapddrhll msvskslcgt
    vvgalidegr idpaqpvtey vpelagsvyd gpsvlqvldm qisidynedy vdpasevqth
    drsagwrtrr dgdpadtyef lttlrgdggt gefqycsant dvlawiverv tglryveals
    tylwakldad rdatitvdqt gfgfanggvs ctardlarvg rmmldggvap ggrvvsqgwv
    esvlaggsre amtdegftsa fpegsytrqw wctgnergnv sgigihgqnl wldprtdsvi
    vklsswpdpd trhwhglqsg illdvsrald av

    >NylB Cupriavidus necator (strain ATCC 43291 / DSM 13513 / N-1) (Ralstonia eutropha)
    MQAQTVTRRT GFGRSRAWLA VALLVAPMSV ALAQGTGQPL VVAEDEVMQG
    FPPPPDKQVS RGSGLRPPYM RWAFRHAREM SPTAGIRHAS QPLALAGQPG
    TELDGTTFAV AGKTARLADY LRDTHTDGFI VLHQGKVVYE RYLAGFGPYQ
    PHIWASMTKS VTGLLAAMLV EEGKLDPQAR LAQYVPELAG NPFGEATVQQ
    NLDMEVPVGY PEGLPPDLGL FGAVGIVPRK ADAPDTIYDF LKVVHATGGR
    DEVGVWYYQN GSPEAVAWAL RRITGKSWAQ LVTERLWSRF ADDDAYTQVD
    RQGTEMASGG MNSTLRDAAR FAEAVRRAAA GDASGGISPA AVRIALQPAG
    NQARFARGNT MPGRDGYGYR NYWFQRNDGD GSIEASGRFG QKIYINPARG
    LTVVKFSANP DGAARATSAA GVRKRDDPGR ALESAEAMVA AALAIHRAVS

    >NylB_1 Bacillus cereus
    MKLKKSPLLL LIITFIFVIT GLGFTYLKHN KTTPSKNNVT KKNWLDDPYL
    RWSYTHMKEF TLINDVKNNP DQIARFPSAL QNLDDFAVQR RFGSTTPLKE
    LLDDNKTDAF VVVHNGQLVY ERYFNGYNES EPHGMASLAK VFTGAIIQSL
    AEENRIDLEK TADTYIKELK NTPFGKATLQ QLMDMQVSVE YPTHGYEHPA
    LENQDAQLYL ASNILPRGKN YDGPMKIYDM LQEAKETAPP GSVFSYNNGS
    TETLAWIIRT ITGKSLAENV SERIWSQIGM EENAYYVTDE TKIEQASAGL
    NATARDMARF GQLLLNNGEY NGKQILPSSI TEDIKNVQQG ELAIGPGASI
    SYHNQWWIPH NEQGAFEVLG SYGQTLYIDP KANMVIVHFS SNATPSNEIH
    SVYSNMYIDI AHHLEKLPQ

    >NylB_2 Bacillus cereus
    MDFKQLENKF EKKKVNTFLV YQKGELTTEY YKTPECANNL YKINSITKSI
    VSILIGIAIG KGYINDIHTP ITKWILNVPK EKSELTIYHL LTMTTGEDWK
    EFGNGVVFPN DFVESENWVQ YILAKPIIEE PATKMNYNSG SSHLLSYIIQ
    KATGMTTEQF AKRYLFDPLE ITEYEWQQDP QGIHVGGFGM KMKSKDLLKL
    GILCLQNGYW QGNEIVSSKW LGESSTALFE TYEHVGAYGY HWWVLNNERF
    HIPYCMYFAM GYGGQYIVII PQLEVVAVIS SHMPKRGLVP LKLFIEHVQE
    NYKFG

    The resulting aligment is depicted below which can be reproduced easily from the above data. It echoes the point that about 12% of the sequences actually align for the same protein.

  3. stcordova: Ahem, enough such features to create Darwin’s abominiable mystery of flowering plants and the potential of large number of orphan genes and systems. We don’t know as much as you suggest we know. The more we learn, the more orphans we discover.In fact we have quite enough such orphans to create very nice nested taxonomic hierarchies.

    Your definition of “orphan” is so flexible as to be useless. Let’s see some specifics: numbers, particulars.

    In any case, it’s a non-sequitur to say orphans of any complexity prove common descent.That’s nonsense.

    Agreed, and fortunately nobody has ever made any such claim.

    I don’t fancy myself as a scholar, just a trouble maker.

    You say that as if it were a good thing. I just take it as a lack of integrity

    But on a related note, I just got this pointer from someone at the NIH.Phylogeny for non-specialists:

    What do you think?

    I think it could be dangerous in unskilled hands. But feel free to try it.

  4. Here is a list of cytochrome-C’s which I pulled off UNIPROT. I’ll provide the Clustal Omega alignment which I put into PHYLIP format and then put into PHYML in the next commnet:

    >LFish1 Neoceratodus forsteri (Australian lungfish) (Ceratodus forsteri)
    MTITRWFFST NHKDIGTLYM IFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVLVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILG SINFITTIIN MKPPAISQYQ TPLFIWSVMI TTILLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    YGMISHIVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG SIKWETPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GGFVHWFPLM
    TGYTLHNTWT KIHFGVMFIG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTVSSIGSLI SLVAVIMLLF IIWEAFAAKR EVMSIELSPT NVEWLHGCPP
    PHHTFEEPAF VQVQTSQR

    >LFish2 Lepidosiren paradoxus (South American lungfish)
    MTITRWLFST NHKDIGTLYM LFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIFNVLVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRLNNM
    SFWLLPPAFL LLLAGSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGMSSILG SINFITTVIN MKPPAASQFQ TPLFIWSVMI TTVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVTY YSGKKEPFGY MGMVWAMIAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG AIKWETPLIW ALGFIFLFTV
    GGLTGVVLAN SSLDIMLHDT YYVVAHFHYV LSMGAVFAIM AGLVHWFPLM
    TGYTLHDTWT KIHFGVTFIG VNLTFFPQHF LGLAGMPRRY SDYPDAYTFW
    NTVSSVGSVI SMVAVMLLLF IIWEAFASKR EVSSIEMTHT NAEWLHGCPP
    PYHTFEEPAF VQTQIVN

    >LFish3 Protopterus annectens (African lungfish)
    MTLTRWLFST NHKDIGTLYM VFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVLVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLAGSGVEA GAGTGWTVYP PLASNLAHAG ASVDLTIFSL
    HLAGVSSILG SINFITTIIN MKPPAASQYQ TPLFIWSVMI TTVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAF YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG AIKWETPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIMLHDT YYVVAHFHYV LSMGAVFAIM GGLMHWFPLM
    TGYTLHDTWT KIHFGVMFLG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTLSSVGSLI SLVAVILLLF IIWEAFASKR EVNSIELIYT NVEWMHGCPP
    PYHTFEEPAF VQIQR

    >LFish4 Protopterus aethiopicus (Marbled lungfish)
    MTLTRWLFST NHKDIGTLYM VFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVLVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLAGSGVEA GAGTGWTVYP PLASNLAHAG ASVDLTIFSL
    HLAGVSSILG SINFITTVIN MKPPAASQYQ TPLFIWSVMI TTVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAF YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG AIKWETPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIMLHDT YYVVAHFHYV LSMGAVFAIM GGLMHWFPLM
    TGYTLHSTWT KIHFGVMFLG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTLSSVGSLI SLVAVILLLF IIWEAFASKR EVDSIELIYT NVEWMHGCPP
    PHHTFEEPAF VQIQR

    >Coel1 Latimeria chalumnae (West Indian ocean coelacanth)
    MMITRWLFST NHKDIGTLYM IFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVVVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSLL LLLASSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILG AINFITTVIN MKPPTMTQYQ TPLFIWSVLV TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG VTKWDTPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIILHDT YYVVAHFHYV LSMGAVFAIM GGLVHWFPLM
    TGYTLHNTWT KIHFGVMFTG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTVSSIGSLI SLIAVIMFMF ILWEAFSAKR EVLIVEMTTT NVEWLHGCPP
    PHHTYEEPAF VQAPR

    >Coel2 Latimeria menadoensis (Indonesian coelacanth)
    MMITRWLFST NHKDIGTLYM IFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVIVTA HAFVMIFFMV MPVMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSLL LLLASSGVEA GAGTGWTVYP PLASNLAHAG ASVDLTIFSL
    HLAGVSSILG AINFITTVIN MKPPTMTQYQ TPLFIWSVLV TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG VTKWDTPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIILHDT YYVVAHFHYV LSMGAVFAIM GGLVHWFPLM
    TGYTLHNTWT KIHFGVMFTG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTVSSIGSLI SLIAVIMFMF ILWEAFSAKR EVLIVEMTTT NVEWLHGCPP
    PHHTYEEPAF VQAR

    >Coel3 Latimeria chalumnae (West Indian ocean coelacanth)
    MMITRWLFST NHKDIGTLYM IFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVVVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSLL LLLASSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILG AINFITTVIN MKPPTMTQYQ TPLFIWSVLV TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG VTKWDTPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIILHDT YYVVAHFHYV LSMGAVFAIM GGLVHWFPLM
    TGYTLHNTWT KIHFGVMFTG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTVSSIGSLI SLIAVIMFMF ILWEAFSAKR EVLIVEMTTT NVEWLHGCPP
    PHHTYEEPAF VQAR

    >Tuna1 Katsuwonus pelamis (Skipjack tuna) (Bonito)
    MAITRWFFST NHKDIGTLYL VFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILG AINFITTIIN MKPAAISQYQ TPLFVWAVLI TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAY YAGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG AVKWETPLLW AIGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIV AAFVHWFPLF
    TGYTLHSTWT KIHFGVMFVG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTISSIGSLI SLVAVIMFLF IIWEAFAAKR EVMSVELTAT NVEWLHGCPP
    PYHTFEEPAF VLVQSD

    >Shark1 Carcharhinus leucas (Bull shark)
    MAINRWLFST NHKDIGTLYL IFGAWAGMVG TALSLLIRAE LGQPGSLLGD
    DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLVPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASAGVEA GAGTGWTVYP PLASNLAHAG PSVDLAIFSL
    XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXMKPPAISQ YQTPLFVWSI
    LVTTILLLLS LPVLAAGITM LLTDRNLNTT FFDPAGGGDP ILYQHLFWFF
    GHPEVYILIL PGFGMISHVV AYYSGKKEPF GYMGMVWAMM AIGLLGFIVW
    AHHMFTVGMD VDTRAYFTSA TMIIAIPTGV KVFSWLATLH GGSIKWDTPL
    LWALGFIFLF TVGGLTGIVL ANSSLDIVLH DTYYVVAHFH YVLSMGAVFA
    IMAGLIHWFP LISGFTLHQT WTKIQFTVMF IGVNLTFFPQ HFLGLAGMPR
    RYSDYPDAYT LWNAISSIGS LISLVAVIML LFIIWEAFAS KREVLSVELP
    HTNVEWLHGC PPPYHTYEEP AFVQVQRPSF

    >Shark2 Glyphis fowlerae (Borneo river shark)
    MAINRWLFST NHKDIGTLYL IFGAWAGMVG TALSLLIRAE LGQPGSLLGD
    DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLVPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASAGVEA GAGTGWTVYP PLASNLAHAG PSVDLAIFSL
    HLAGVSSILA SINFITTIIN MKPPAISQYQ TPLFVWSILV TTILLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHVVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG SIKWDTPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM AGLIHWFPLI
    SGFTLHQTWT KIQFTVMFIG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NAISSIGSLI SLVAVIMLLF IIWEAFASKR EVLSVELPHT NVEWLHGCPP
    PYHTYEEPAF VQVQRPSF

    >Bird1 Trichobilharzia regenti (Nasal bird schistosome)
    MILSYFSWLV SLDHKRIGVI YFLLGLWGGF IGLGLSLLIR LNFCEPYYNL
    VPSEIYNYLI TNHGIAMIFF FLMPVLIGGF GNYLLPFLLG LDDLALPRLN
    SLSVWLMVPS MFYMELSLVY GAGVGWTFYP PLSIQSSMGV GVDYLMFSLH
    LAGVSSLLGS VNFITTILLN LSFRVSVIVW SYLFTSILLL LSLPVLAAGI
    TMLLFDRNFG TAFFEPCGGG DPILFQHLFW FFGHPEVYVL ILPGFGVVSH
    ICMNLSNNDS SFGYYGLVCA MGSIVCLGSV VWAHHMFMVG LDVKTAVFFS
    SVTMVIGIPT GIKVFSWLYM LGTSYLRGVE PIVLWVLGFI FLFTVGGVTG
    IVLSASVLDS LFHDTWFVIA HFHYVLSLGS YSTVVISLIW WWPVIIGYSL
    NKYLLYGHWF LSMVGFNLCF FPMHYLGMHG LPRRVCCYDP EFYWVNVVCS
    VGGVLSVVSS MIFLFILWES ITVGNRVLGL WGSGSFPLNV VTVPTPYHAS
    YMSSVKLWVT I

    >Human
    MFADRWLFST NHKDIGTLYL LFGAWAGVLG TALSLLIRAE LGQPGNLLGN
    DHIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLVPLMIGAP DMAFPRMNNM
    SFWLLPPSLL LLLASAMVEA GAGTGWTVYP PLAGNYSHPG ASVDLTIFSL
    HLAGVSSILG AINFITTIIN MKPPAMTQYQ TPLFVWSVLI TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVTY YSGKKEPFGY MGMVWAMMSI GFLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGS NMKWSAAVLW ALGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GGFIHWFPLF
    SGYTLDQTYA KIHFTIMFIG VNLTFFPQHF LGLSGMPRRY SDYPDAYTTW
    NILSSVGSFI SLTAVMLMIF MIWEAFASKR KVLMVEEPSM NLEWLYGCPP
    PYHTFEEPVY MKS

    >Kangaroo Macropus giganteus (Eastern gray kangaroo)
    MFITRWLFST NHKDIGTLYL LFGAWAGMVG TALSLLIRAE LGQPGTLLGD
    DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLVPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASSTVEA GAGTGWTVYP PLAGNLAHAG ASVDLAIFSL
    HLAGVSSILG AINFITTIIN MKPPALSQYQ TPLFVWSVMI TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVTY YSGKKEPFGY MGMVWAMMSI GFLGFIVWAH HMFTVGLDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG NIKWSPALLW ALGFIFLFTI
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GGFVHWFPLF
    TGYTLNDLWA KIHFSIMFVG VNMTFFPQHF LGLSGMPRRY SDYPDAYTTW
    NVISSIGSFI SLTAVILMVF IIWEAFASKR EVSTVELTTT NIEWLHGCPP
    PYHTFEQPAF IKV

    >Elephant Loxodonta africana (African elephant)
    MFANRWLYST NHKDIGTLYL LFGAWAGMVG TAFSILIRAE LGQPGSLLGD
    DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASSMVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILS AINFITTIIN MKPPAMSQYH MPLFVWSILI TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMVSHIVTY YSGKKEPFGY MGMVWAMMSI GFLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG NIKWSPAMMW ALGFIFLFTI
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GGFIHWFPLF
    SGYTLNYTWA KIQFLVMFIG VNLTFFPQHF LGLSGMPRRY SDYPDAYTAW
    NTASSMGSFI SLVAVILMVF MIWEAFASKR EVSVMELTTT NVEWLNGCPP
    PHHTFEEPAY VKSNS

  5. So here is the “phylogeny” generated. Doesn’t look to me like one can unequivocally say Birds and Mammals descendend from Lunfish and Coelecanth-like creatures does it?

  6. I wrote in the OP:

    Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

    I just proved my point with the diagram of the Cytochrome-C “phylogenies”.

  7. Sal:

    I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

    First, your revulsion is entirely irrelevant. Second, the Sarcopterygii clade is a clade, not an organism. It doesn’t “look like a coelacanth”.

    I don’t fancy myself as a scholar, just a trouble maker.

    You’re just a confused guy, addled by the Jebus Effect, struggling in futility against science.

  8. stcordova:
    So here is the “phylogeny” generated.Doesn’t look to me like one can unequivocally say Birds and Mammals descendend from Lunfish and Coelecanth-like creatures does it?

    There is clearly something wrong with your analysis, but it’s hard to tell just what without knowing the details of how it was performed. Still, one thing: your “bird” is actually a flatworm. See what I mean about a little knowledge being dangerous?

  9. John, to Sal:

    Still, one thing: your “bird” is actually a flatworm.

    Which nicely corroborates my observation:

    You’re just a confused guy, addled by the Jebus Effect, struggling in futility against science.

  10. Still, one thing: your “bird” is actually a flatworm. See what I mean about a little knowledge being dangerous?

    See, this is why I’m here. I learn something, and you don’t. I have my ideas improved on and you don’t. Suffice to say, I don’t think you’ve learned much in this discussion, nor have you come any closer to improving your theses.

    If I remove the flatworm, and do you think it will make humans “nest” within lungfish and coelecanths (much closer to what a Sarcopterygii would actually look like).

    Anyway, thanks a plenty for cleaning up my error.

    There is clearly something wrong with your analysis, but it’s hard to tell just what without knowing the details of how it was performed.

    Why don’t we agree on some proteins? Like aaRS, Topoisomerases.

  11. Sal, to John:

    See, this is why I’m here. I learn something, and you don’t. I have my ideas improved on and you don’t.

    If you had something to teach him, I’m sure he could learn it. As it is, the brighter folks here are just correcting your mistakes, Sal.

  12. Here I removed the flatworm, does it make humans nest with Sarcopterygiians (like Lungfish and Coelecanths)? Nope. Like I said it’s revolting to taxonomy to say humans are Sarcopterygiians.

    You may have scored on style points with the flatworm, but it’s a mistake I don’t have to make again thanks to you. On the otherhand, I won my argument on substance, especially now with the improved version you actually helped create. Thank you very much!

  13. stcordova: See, this is why I’m here. I learn something, and you don’t. I have my ideas improved on and you don’t. Suffice to say, I don’t think you’ve learned much in this discussion, nor have you come any closer to improving your theses.

    That assumes you have anything to teach me and that my “theses” need any improvement.

    If I remove the flatworm, and do you think it will make humans “nest” within lungfish and coelecanths (much closer to what a Sarcopterygii would actually look like).

    You are unfamiliar with the meaning of “Sarcopterygii”; not a problem unless you assume you actually do know. One very dirty analysis of one protein in a few species isn’t going to help. Supposing that your rudimentary attempt should overturn decades of real phylogenetic analyses isn’t going to help.

    Anyway, thanks a plenty for cleaning up my error.

    If only some of this would teach you just a little humility, it would be worthwhile.

    Why don’t we agree on some proteins? Like aaRS, Topoisomerases.

    Or you could just look for published papers that already have done that sort of thing.

  14. stcordova:
    Here I removed the flatworm,does it make humans nest with Sarcopterygiians (like Lungfish and Coelecanths)?Nope.Like I said it’s revolting to taxonomy to say humans are Sarcopterygiians.

    You may have scored on style points with the flatworm, but it’s a mistake I don’t have to make again thanks to you.On the otherhand, I won my argument on substance, especially now with the improved version you actually helped create.Thank you very much!

    Your delusions of adequacy are tiresome, and your misplaced triumphalism equally so. How much of your tree do you think represents real phylogeny and how much is something else? If it’s something else, what is that?

  15. John Harshman: I just take it as a lack of integrity

    John would know all about that. So we should take this seriously.

    John Harshman: If only some of this would teach you just a little humility, it would be worthwhile.

    Do as John says, not as John does.

    This is the same John Harshman who, when it was pointed out to him that he was making up just so stories, didn’t want to hear it.

  16. keiths: DNA_Jock,

    You are making the same mistake as Sal. Sal Cordova. That ought to give you pause.

    No, actually, I am not.

    He’s making it in support of creationism, and you in support of guided evolution, but it’s essentially the same mistake.

    Oh, I’m not supporting guided evolution – I am not aware of any evidence to support that concept. I am merely trying to explain to you how (partially) guided evolution could lead to the ONH that we observe.

    [snip] Neither of you has a hotline to the Designer/Guider (if one even exists), or any special insight into his goals, his abilities, his limitations, and his preferred mode of operation.

    Well then, that makes three of us, doesn’t it?

    The number of ways in which he could produce an ONH are vastly outnumbered by the ways in which he could fail to do so. Thus there is no reason to expect that his activities will produce an ONH.

    ^This^ is where your dichotomous thinking has gotten you confused. The best explanation that I can arrive at is that you are considering the hierarchy of changes introduced by the guider in isolation. That’s wrong. We agree that we have descent with modification, which produces a mind-blowingly powerful phylogenetic signal. Buried inside this, we have some aberrations, which we ascribe to convergent evolution (or HGT across taxons…). The sum total of all of these anomalies does not lead sane people to doubt the fact of common descent, because the signal is still there, loud and clear. Because there’s a lot of signal, the analysis can tolerate a pretty large number of anomalies…
    Now, the guider’s tinkering, in and of itself, may or may not produce an ONH, depending on his (unknown) preferred mode of operation. Doesn’t really matter, since even a goodly dose of non-hierarchical tinkering would not stop the John Harshman’s of this world from revealing an ONH, albeit one with some anomalies.
    If, and only if, the guider was motivated to deliberately obscure the phylogenetic signal would we NOT expect to see such a signal. It isn’t me that’s making assumptions about the goals and abilities of the guider.
    It seems that only you fail to understand this. Well, maybe you and phoodoo. That ought to give you pause.

  17. John Harshman:

    Or you could just look for published papers that already have done that sort of thing.

    What makes you think I haven’t. It had the anomaly of lack of sequence divergence we’ve been arguing about. You seem to be under the mistaken impression population sizes doesn’t have a radical impact on the applicability of coalescence theory. Like I said, you’re don’t seem to be learning anything in this discussion.

  18. stcordova: What makes you think I haven’t.

    The fact that you have never mentioned any.

    It had the anomaly of lack of sequence divergence we’ve been arguing about.

    What do you mean by “it”? And are we still talking about vertebrates? If not, why did you just change the subject?

    You seem to be under the mistaken impression population sizes doesn’t have a radical impact on the applicability of coalescence theory. Like I said, you’re don’t seem to be learning anything in this discussion.

    That’s right. Population size doesn’t have a radical impact on the applicability of coalescence theory, though it does have an impact on coalescence time, quite a different thing. Like I said, perhaps you have nothing to teach.

  19. John Harshman:

    Population size doesn’t have a radical impact on the applicability of coalescence theory, though it does have an impact on coalescence time, quite a different thing.

    If population size affects coalescence time, then don’t apply it to population sizes that would drive the coalescence time beyond the Big-Bang, so it does have an impact on the applicability. Like I said, you’re not learning anything, you’re just mincing words.

  20. John Harshman: Like I said, perhaps you have nothing to teach.

    He’d have to learn how to evaluate evidence properly first.

    Pascal’s Wager comes after, if it is to be used at all.

    Sal learns, but he moves away from what the evidence shows, not toward it. Hence his more recent belief in the young earth, an even less supportable idea than the vapid ID belief.

    Glen Davidson

  21. stcordova: If population size affects coalescence time, then don’t apply it to population sizes that would drive the coalescence time beyond the Big-Bang, so it does have an impact on the applicability.

    We perhaps mean different things by “applicability”. I don’t think this hypothetical population you’re talking about has a constant size. I think it’s been through a huge number of bottlenecks.

  22. DNA_Jock,

    We agree that we have descent with modification, which produces a mind-blowingly powerful phylogenetic signal. Buried inside this, we have some aberrations, which we ascribe to convergent evolution (or HGT across taxons…).

    I would agree there is a powerful phylogenetic signal except for convergent evolution and random gene loss. I don’t see any reason that signal could not be the result of common design.

    Sal’s flower looks more like common design versus common descent because common design does not have the problem of explaining these anomalies such as gene loss.

    Common descent not being able to account for new genes makes it a very poor explanation of life’s diversity. I agree with keiths that unless you can explain the evidence with reproduction alone then common descent is not an accurate description of the data.

  23. If you see a comment be me, above, with a hopelessly-unreadable tree you should ignore it (I have requested its deletion). I will repost that when I have time to figure out how to include a diagram of the tree that is legible.

    Short summary: a protein ML run confirms Sal’s tree, but a bootstrap analysis shows that all the critical interior branches that distinguish it from the usual consensus vertebrate tree are not significantly supported.

  24. colewd:
    DNA_Jock,
    I don’t see any reason that signal could not be the result of common design.

    Of course not. Anything at all could be the result of common design; it’s a meaningless phrase that makes no predictions at all.

    Sal’s flower looks more like common design versus common descent because common design does not have the problem of explaining these anomalies such as gene loss.

    That’s because common design doesn’t have the problem of explaining anything at all. Is that actually a virtue? Anyway, gene loss isn’t an anomaly. Didn’t you see my optimization of gene loss onto a tree? Almost all the bits of Sal’s flower fit the standard tree perfectly while only a comparative few don’t. Now why should that be?

    Common descent not being able to account for new genes makes it a very poor explanation of life’s diversity.

    Common descent doesn’t attempt to account for new genes, only for their patterns of distribution. Common descent doesn’t attempt to explain life’s diversity either, only why that diversity fits into a tree. You understand so little and assume so much that it’s hard to talk to you.

    I agree with keiths that unless you can explain the evidence with reproduction alone then common descent is not an accurate description of the data.

    I don’t think you understand what keiths was trying to say or what “accurate description of the data” means.

  25. DNA_Jock: I am merely trying to explain to you how (partially) guided evolution could lead to the ONH that we observe.

    Careful examination shows that the leaves of this tree form a nested hierarchy. If we watch the tree closely over a period of time, the branching process appears to be spontaneous. However, from this information alone, we cannot exclude design.

    Topiary

  26. Zachriel: Careful examination shows that the leaves of this tree form a nested hierarchy. If we watch the tree closely over a period of time, the branching process appears to be spontaneous. However, from this information alone, we cannot exclude design.

    The leaves of that tree don’t appear to form a nested hierarchy, which is a problem for your analogy.

  27. John Harshman: The leaves of that tree don’t appear to form a nested hierarchy, which is a problem for your analogy.

    They appear to me to form a nested hierarchy. You think they are just hanging there in space without being descended from a common ancestral cell?

  28. John Harshman,

    As I understand Zachriel’s analogy, the leaves of this tree _do_ form a nested hierarchy: their lineage within the branching hierachy. Perhaps I am missing something.
    But Zachriel, AIUI, raises an excellent point: the guider could restrict herself to selective, and extremely crafty, culling. Desirable species could have their principal competitors wiped out; it’s guided evolution, but it has zero effect on the phylogenetic signal-to-noise ratio that we observe.
    Chicxulub, anyone?

  29. John Harshman,

    Of course not. Anything at all could be the result of common design; it’s a meaningless phrase that makes no predictions at all.

    It’s an argument from analogy with clear strengths and weaknesses. The make up of cells show consistency in how things are accomplished which I would predict from design. An example of this is cell regulation. When regulating cell division a destruction mechanism is used to down regulate cell division. The exact same strategy is used to down regulate vascular growth which prevents metastasis.

    The transcription translation mechanism is common across life and splicing is common across all eukaryotic life. These are common designs. The prediction is that these mechanisms will be common across life including both plants and animals.

    That’s because common design doesn’t have the problem of explaining anything at all. Is that actually a virtue?

    It explains commonality across life and the repeated use of design strategies. If I were to try and find how a portion of a protein based cellular function was regulated I would predict a destruction mechanism.

    Common descent doesn’t attempt to account for new genes, only for their patterns of distribution. Common descent doesn’t attempt to explain life’s diversity either, only why that diversity fits into a tree. You understand so little and assume so much that it’s hard to talk to you.

    Common design does explain life’s diversity and the appearance of new genes. Both the sequential nature of DNA and additional sequencing capability of alternative splicing are effective strategies in creating diversity because they utilize a mathematical sequence.

    I don’t think you understand what keiths was trying to say or what “accurate description of the data” means.

    I think you are understandably trying to hold on to the historical terminology when it needs to be forced to fit the data. Inconvenient truths (convergent evolution) should be challenging the status quo and they are not.

    Anyway, gene loss isn’t an anomaly. Didn’t you see my optimization of gene loss onto a tree? Almost all the bits of Sal’s flower fit the standard tree perfectly while only a comparative few don’t. Now why should that be?

    I think gene loss is an assumption you are making based on assuming common descent. The few that don’t breaks the pattern you are trying to demonstrate.

  30. colewd:
    John Harshman,

    It’s an argument from analogy with clear strengths and weaknesses.

    It’s a weak analogy that tells us nothing meaningful. Clearly life is not like what we make, so IDists try to both claim that it’s like what is seen to be designed and that it is really quite different and better. Meanwhile, you ignore all of the evidence that is counter to design, like the non-portability of “designs” across unrelated lineages in vertebrates.

    The make up of cells show consistency in how things are accomplished which I would predict from design.

    Too much consistency and too little. You predictably ignore the details and wave your hand, saying that it is what you’d predict from design. Well, what wouldn’t you “predict”? You’re impervious to evidence.

    So there’s consistency within lines, which is why bats only get modified mammal forelimbs as wings. There’s bat inconsistency with bird wings, since there’s no inheritance shared with birds (other than homologies much earlier than flight). Real designers don’t observe such limits. You’ve heard all of this before, but you don’t care about the evidence (and seem slow to pick up on facts and arguments), hence the same bland BS regardless of the facts.

    An example of this is cell regulation.When regulating cell division a destruction mechanism is used to down regulate cell division.The exact same strategy is used to down regulate vascular growth which prevents metastasis.

    Yes, you’d really expect that from evolution. Why would a designer not do something different? Maybe it would, maybe it wouldn’t, but what we don’t see are the effects expected from a designer that wouldn’t be expected of evolution.

    The transcription translation mechanism is common across life and splicing is common across all eukaryotic life.These are common designs.The prediction is that these mechanisms will be common across life including both plants and animals.

    It’s an ex post facto “prediction.” God would not be so limited as evolution, which is pretty much stuck with inheritance, plus tinkering.

    It explains commonality across life and the repeated use of design strategies.If I were to try and find how a portion of a protein based cellular function was regulated I would predict a destruction mechanism.

    Who cares what you’d “predict”? You’ve been shown how life deviates substantially from what known designers do, and yet you just “predict” whatever is seen as “common design” without you caring in the least about how life follows the limitations of heredity, as known designers don’t.

    Common design does explain life’s diversity and the appearance of new genes.Both the sequential nature of DNA and additional sequencing capability of alternative splicing are effective strategies in creating diversity because they utilize a mathematical sequence.

    You’d need some good evidence to properly claim that alternative splicing utilize a mathematical sequence, as well as DNA sequences themselves. Any evidence for that?

    I think you are understandably trying to hold on to the historical terminology when it needs to be forced to fit the data.Inconvenient truths (convergent evolution) should be challenging the status quo and they are not.

    I suppose that has something to do with the fact that you merely assert that convergent evolution is a problem for common descent, and you utterly lack any kind of evidential basis for that. Either make a cogent evidence-based argument or learn how to at least quit asserting what you can’t support. The fact that you imbibe BS from IDiots is no argument for anything.

    I think gene loss is an assumption you are making based on assuming common descent.

    Since we have many pseudogenes of lost genes, that’s utter BS. Quit making demonstrably false accusations.

    The few that don’t breaks the pattern you are trying to demonstrate.

    Makes no sense.

    Glen Davidson

  31. Joe Felsenstein,

    FWIW, we’re finally covering phylolgeny in my graduate Bio-Informatics class this evening at the NIH. Phylogeny will probably be 1.5 lectures, total.

    Today the professor showcased your book, called it “state of the art 10 years ago” with the implication your book is now canon.

  32. colewd: Me: Anyway, gene loss isn’t an anomaly. Didn’t you see my optimization of gene loss onto a tree? Almost all the bits of Sal’s flower fit the standard tree perfectly while only a comparative few don’t. Now why should that be?

    Bill: I think gene loss is an assumption you are making based on assuming common descent. The few that don’t breaks the pattern you are trying to demonstrate.

    I see you didn’t answer the question. Now why should that be?

  33. DNA_Jock:

    I am merely trying to explain to you how (partially) guided evolution could lead to the ONH that we observe.

    Why explain something that a) is obvious and b) I’ve never disputed?

    Once again:

    He’s [Sal is] saying “Look, here’s how the Designer could have produced an objective nested hierarchy,” as if we had ever argued otherwise. You are saying “Look, here’s how the Guider could have produced an objective nested hierarchy, as if I had ever argued otherwise.

    Of course it’s logically possible for a Designer, or a Guider, to do those things. The question is whether the two of you can justifiably assume that he’ll do those things.

    The answer is clearly ‘no’. Neither of you has a hotline to the Designer/Guider (if one even exists), or any special insight into his goals, his abilities, his limitations, and his preferred mode of operation.

    The number of ways in which he could produce an ONH are vastly outnumbered by the ways in which he could fail to do so. Thus there is no reason to expect that his activities will produce an ONH.

    So instead of stating the obvious, which is that a Designer/Guider could produce an ONH, you need to tell us why he would be expected to do so.

    Good luck.

  34. Zachriel,

    See my response to DNA_Jock above.

    My claim is not that it is logically impossible for guided evolution (or separate creation, for that matter) to produce an inferable ONH. Instead, I’m claiming that neither of them should be expected to produce an inferable ONH.

    That’s why I disputed John’s statement:

    Guided evolution predicts a nested hierarchy as long as it occurs within a context of common descent.

    To infer guided evolution from the ONH is as silly as inferring the Rain Fairy from the meteorological evidence. Neither of them is ruled out as a matter of sheer logic, but we recognize their goofiness based on the unwarranted assumptions they require.

  35. keiths: Instead, I’m claiming that neither of them should be expected to produce an inferable ONH.

    I simply disagree. We have well-known examples of guided evolution producing ONH. Case in point: selective breeding. We can still trace the evolution of all sorts of animal and plants that have been selectively breeded for millenia, to their wild-type ancestors, because they still fit very well into the nesting hiearchy.

  36. keiths:

    My claim is not that it is logically impossible for guided evolution (or separate creation, for that matter) to produce an inferable ONH. Instead, I’m claiming that neither of them should be expected to produce an inferable ONH.

    Rumraket:

    I simply disagree. We have well-known examples of guided evolution producing ONH. Case in point: selective breeding. We can still trace the evolution of all sorts of animal and plants that have been selectively breeded for millenia, to their wild-type ancestors, because they still fit very well into the nesting hiearchy.

    That’s bad logic. The fact that guided evolution can produce an ONH, and that it has been observed to do so in the past, does not mean that it should be expected to do so. Selective breeding is not the only possible form of guided evolution, not by a long shot. Why assume that the Guider would operate in that way, whether by choice or necessity? (Particular when we know who the IDers think, or hope, the big-G Guider actually is.)

    As I pointed out to DNA_Jock:

    Neither of you has a hotline to the Designer/Guider (if one even exists), or any special insight into his goals, his abilities, his limitations, and his preferred mode of operation.

  37. colewd: The transcription translation mechanism is common across life and splicing is common across all eukaryotic life. These are common designs. The prediction is that these mechanisms will be common across life including both plants and animals.

    You just stated that splicing is restricted to eukaryotes, so in fact it is not common across life. In fact, lots of features are variable.

    You are missing an explanation for the fact that there is abundant variation both between and within lineages. Why do bacteria have use for a different mechanism of transcription? Why is splicing not widespread in prokaryotes? Different manufacturer?

  38. keiths,

    You really seem to be completely unable to read for comprehension.
    No-one amongst John Harshman, Rumraket, Zachriel and myself is arguing that one should “infer guided evolution” based on the available data. I have explicitly stated

    I am not aware of any evidence to support that concept.

    Y’know, the sentence immediately preceding the one you quoted.
    John’s statement, which you chose to dispute:

    Guided evolution predicts a nested hierarchy as long as it occurs within a context of common descent.

    is correct. The only assumption about the guider that is required is that the guider does not deliberately (and almost exhaustively) obliterate the phylogenetic signal.
    We all are agreed, I believe, that there is no reason to believe that the actions of a guider should in and of themselves produce an ONH. In this regard, your

    The number of ways in which he could produce an ONH are vastly outnumbered by the ways in which he could fail to do so.

    is correct, but if this guiding occurs within the context of common descent, then we would expect it to produce an ONH.
    This has been explained to you multiple times by multiple posters, yet you fail to address their points, merely rabbiting what you said previously. Please consider the possibility that these other posters (including a phylogeneticist, FFS) might have a point.

  39. DNA_Jock,

    You really seem to be completely unable to read for comprehension.
    No-one amongst John Harshman, Rumraket, Zachriel and myself is arguing that one should “infer guided evolution” based on the available data.

    Instead of simply assuming that the problem lies on my end, why not double-check yourself? It’s part of being a good skeptic. Re-read my comments.

    Nowhere do I claim that John, or Zachriel, or Mikkel, or you have argued that we should infer guided evolution based on the available data. If you actually believed that, you’d be IDers! I obviously do not think the four of you are IDers.

    …if this guiding occurs within the context of common descent, then we would expect it to produce an ONH.

    That’s incorrect. I’ll explain why (again) later today. In the meantime, try to cultivate a bit of self-skepticism so that you’ll be open to actually hearing my argument when it comes, rather than projecting your expectations onto it.

  40. keiths: Nowhere do I claim that John, or Zachriel, or Mikkel, or you have argued that we should infer guided evolution based on the available data.

    Is that so?

    keiths: That’s why I disputed John’s statement:

    Guided evolution predicts a nested hierarchy as long as it occurs within a context of common descent.

    To infer guided evolution from the ONH is as silly as inferring the Rain Fairy from the meteorological evidence.

    Then why bring it up?

  41. DNA_Jock: As I understand Zachriel’s analogy, the leaves of this tree _do_ form a nested hierarchy: their lineage within the branching hierachy.

    That is correct. ETA: Something we can determine by careful examination of the branches. ETA: Or possibly from the genetics of the leaves.

    DNA_Jock: the guider could restrict herself to selective, and extremely crafty, culling. Desirable species could have their principal competitors wiped out; it’s guided evolution, but it has zero effect on the phylogenetic signal-to-noise ratio that we observe.

    That is correct. You can’t determined the cause of the shape of the tree without additional information beyond that of the existence of a nested hierarchy. You could be looking at a natural process, or you could be looking at topiary.

  42. keiths: The fact that guided evolution can produce an ONH, and that it has been observed to do so in the past, does not mean that it should be expected to do so.

    LoL. All the evidence available points to guided evolution producing a nested hierarchy, but that’s no reason to expect a nested hierarchy from guided evolution.

    Now really, who can argue with logic as unassailable as that?

    There is, likewise, no reason to expect a nested hierarchy from unguided evolution. We have zero evidence that unguided evolution can produce an ONH, and it has never been observed to do so in the past.

  43. Because of HGT, common descent of the organism isn’t always common descent of the gene in question.

    Of immediate interest to the nylonase research project Flavobacteria KI72 and Agromyces KYR5 have a gene, nylonase nylB that creates proteins that is identical in 391 out of 392 residues.

    Back in March, before we considered HGT, Dr. Sanford and I were initially enthusiastic for the first few hours at the discovery in the literature of Agromyces KYR5’s nylB gene as it superficially suggested the nylonase was more ancient than 1935 but then when I tracked the geography and looked at how closely the genes resembled each other, I concluded it was far too similar to rule out HGT, although the way it was laid out on the KYR5 chromosome would make the HGT challenging. At that point, in despair I went on to look for other tools to establish “conservation” of structural motifs that didn’t have too strong a sequence similarity to establish a pre-1935 origin of nylonase NylB. So therein is a case where it is possible common descent of the organism and common descent of the gene are not the same thing.

    I thankfully stumbled first on the fact Trypsins and other serine hydrolases could act as nylonases, and then quite by providence, I discovered thousand, maybe not tens of thousands of nylonase homologs, many with the Beta Lactamase fold that Doug Axe made a point of contention.

    My present time at the NIH is to improve the nylonase project and there have been some nice side benefits to learning the various bio-informatics tools which I have shown examples of like MUSCLE and PSI-BLAST.

    But back to HGT or common design. Being a creationist, I’m not that much concerned with the Universal common descent of creatures. I accept some HGT, in fact for my present research I find it an important consideration. But I’m not concerned with building a tree of life nor orchard of life.

    The phylogenetic diagrams, especially the unrooted variety on individual genes is sufficient to show nested similarities for my purposes. I suspect the nested hierarchies created by individual genes will not line up with the supposed species descent because of HGT and definitely because of common design.

    So I don’t believe there is a UNIQUE taxononmic nested hierarchy, but multiple conflicting taxonomic nested hierarchies as would be absolutely demonstrable by diagrams such as this one:

    http://www.sci-news.com/genetics/article01036.html

    If we made a molecular “phylogeny” with genes shared by chickens and man it might look different than the molecular phylogeny with genes shared by mice and men. From a common design+HGT model, the multiple conflicting molecular taxnomic nested hierarchies are not a problem as most common design proponents are creationists and don’t really care about trying to describe Common Ancestors which we don’t believe existed anyway.

  44. To highlight the problem of HGT, consider the phylogenetic diagram I put together of various NylB proteins. It would be absurd to try to create a phylogeny of the bacteria based on the NylB Gene. For example, look at Bacillus cereus NylB_1 vs Bacillus cereus NylB_2!

    Or look at the clustering of NylB on Pseudomonas.

    It first alarmed me when Dr. Sanford said there aren’t really any bacterial species. What he meant was it’s hard to say bacteria have stable geneomes because of all the HGT going on. It become hard to define species because of this problem.

    That said, for the purposes of common design, it suffices to show a conserved motif, whatever the causes and whatever strange way it is distributed amongst species.

    You can enlarge the image here:

    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/phylogenetic_sample.png

    You can see the parallel discussion on nylonases here:

    http://theskepticalzone.com/wp/invited-responses-to-my-nylonase-research-and-the-question-of-new-proteins-without-gods-help/

  45. GlenDavidson,

    It’s a weak analogy that tells us nothing meaningful. Clearly life is not like what we make, so IDists try to both claim that it’s like what is seen to be designed and that it is really quite different and better. Meanwhile, you ignore all of the evidence that is counter to design, like the non-portability of “designs” across unrelated lineages in vertebrates.

    The transcription translation mechanism along with DNA makes life portable. To change organisms requires a change to the nucleotide sequence. The hardware gets changed simply by a change in software as an analogy.

    It’s an ex post facto “prediction.” God would not be so limited as evolution, which is pretty much stuck with inheritance, plus tinkering.

    Flight is inheritance plus tinkering? Flight clearly requires design.

    You’d need some good evidence to properly claim that alternative splicing utilize a mathematical sequence, as well as DNA sequences themselves. Any evidence for that?

    A sequence is a set of objects. Here are the objects in DNA Proteins and splicing.

    DNA object= Nucleic Acid
    Protein object= Amino Acid
    Splicing object= Exon

Leave a Reply